Women were also more likely than men to experience both threats and actual violence.
Forty per cent of female leaders were threatened with violence, compared to 34 per cent of male leaders.
Actual violence was reported by 43 per cent of female leaders, compared to 38 per cent of male leaders.
High levels of verbal abuse were also reported, with 59 per cent the victims of gossip and slander, 38 per cent receiving bullying, 13 per cent unpleasant teasing and 3 per cent sexual harassment.
School leader bullying rates were also much higher than the general population, and unpleasant teasing slightly higher. Both rates had increased from 2016.
Those doing the bullying were other adults 96 per cent of time, most often parents, but also colleagues, managers or subordinates.
The Offensive Behaviour in Schools survey is the third part of a wider report, following others titled Discrimination and Burnout.
NZEI Te Riu Roa president Lynda Stuart said the findings raised serious safety and wellbeing issues.
"Along with their heavy workloads, school leaders are also having to cope with behaviours such as threats of violence, actual violence, bullying, conflicts, gossip and slander.
"Schools need to be safe places for everyone: creative and compassionate spaces where children can meet their potential, and teachers and leaders can do their jobs free of all types of harassment.
"There are two parallel issues going on here. One is children with learning difficulties trying to access the help and support that they and their families need, and the other is adults whose behaviour in a learning environment is sometimes unacceptable.
"We are not trying to apportion blame here, we are making recommendations on how to move forward, and this needs resources and funding to urgently address the problem."
NZEI Te Riu Roa recommended resourcing and staffing be increased to support the growing number of students with challenging behaviours.
It also called for school boards to uphold safe environments in schools, a mediation service for families and schools, regular teacher training in responding to violent situations, increased mentoring and counselling, and more thorough investigations of violent incidents and bullying.